This is the git repo that contains all code written during the summer of 2014 for the P20 internship.

• chromoprocessor/chromoprocessor.py: processes multiple bam files in parallel
• tovcf/tovcf.py: converts an Excel file to a VCF file
• parallel/chromosplit.py: processes a single bam file in parallel

• vcfparse/vcfparse.py: extracts the specified regions from a VCF file
• vcfrename/vcfrename.py: renames the sample columns in a VCF file

• graph/: this directory contains R scripts written for specific data, they aren't meant to be general

• install.py: installs the Python modules needed for the programs in this repo

Most of the Python programs depend on external libraries and modules. Each dependency is listed in the README for that particular program. However, if you plan on using all the programs at some point in time, you can run install.py and it will install all the Python modules that chromoprocessor, vcfparse, and tovcf need for the user.

Note: install.py also installs pip